PDBCat can be used to manipulate and process PDB files using commonly available
text-processing tools such as Perl, awk, etc. The Brookhaven Protein Data Bank
stores atomic coordinate information for protein structures in a column-based
format which is designed to be read easily read by FORTRAN programs. PDBCat
converts the ATOM and HETATM records of PDB files from this column-based format
to a field-based one that is more easily processed by standard Unix tools.

SODIUM places the required number of sodium ions around a (simulated) system of
electric charges, e.g., the atoms of a biological macromolecule (protein, DNA,
protein/DNA complex). The ions are placed in the nodes of a cubic grid in which
the electrostatic energy achieves the smallest values. The energy is
re-computed after placement of each ion. A simple Coulombic formula is used for
the energy. The coordinates of the placed ions are printed out in the PDB
format for further usage. Trivial modifications to the program should allow
the placement of any combination of multivalent ions of different charges.

Wat2ions is complementary to DelPhi, the renowned solver of the
Poisson-Boltzmann equation. The electrostatic potential map pre-computed by
DelPhi is used to replace a certain number of the water molecules of the bath,
surrounding a solvated macromolecule, with ions. The potential on the oxygens
of the water molecules is estimated using a 3D cubic spline interpolation of
the pre-computed potential. The waters with the largest potential are replaced
with chlorides, and the waters with the smallest potential, with sodii. No two
ions are placed closer than a certain distance to each other. The coordinates
of the macromolecule, the water bath (except the replaced waters), and the
placed ions are output to a new PDB file.

GNotary is a set of Python scripts that implement an asynchronous
digital notary service. Anybody who needs certification of any digital
document creates a message digest (like MD5 or RIPEMD160) of that
document and submits it to the GNotary service by email. GNotary signs
this email digitally (using GnuPG), retains a copy of the certified and
time stamped message, and mails it back to the sender, optionally
with the public key attached to allow the sender to verify the signed
document. At regular intervals, the GNotary server creates message
digests of its own logs and distributes them among other GNotary
servers, thus making it virtually impossible to forge the chain of
evidence that authenticates a submitted document.

MultiSlice RTP is a radiotherapy treatment
planning and medical image processing system
developed for Silicon Graphics MIPS architecture
systems and the IRIX operating system (5.3 and
above). It allows you to manipulate upto 20 2D CT
image slices as one 3D slice and run bulk batch
processing algorithms on the images loaded.
Written in C and linked against the MOTIF toolkit,
it also runs on Xfree/Linux/Lesstif and can load
RAW CT images from a CT scanner directly.

MrGrid is a MR file analyser for statistical
supported counting of surfaces and volumes
contained in MR images. It supports remapping of
the grayscale images into false color images to
appreciate the full dynamic range of information
contained in the image.